Objective To compare the value of 16S rDNA sequencing and traditional culture in the detection of pathogens in liver and renal abscess, analyze characteristics and composition of pathogens in liver and renal abscess. Methods Abscess drainage fluid of 32 patients (24 cases of liver abscess and 8 cases of renal abscess) who underwent percutaneous drainage in a hospital from December 2019 to December 2020 were collected, pathogens were identified by traditional culture and 16S rDNA sequencing, flora characteristics of liver and renal abscess were compared and analyzed. Results The traditional culture results of abscess drainage fluid were 26 cases (81.25%) positive and 6 cases (18.75%) negative (including 3 cases of liver abscess and 3 cases of renal abscess), while the positive rate of 16S rDNA sequencing was 100%. The abundance of microbial flora in liver and renal abscess groups was similar, but the stacked bar chart and principal component analysis (PCA) indicated significant differences in the composition of pathogens between two groups. Linear discriminant analysis (LDA) showed that the flora of liver abscess group was mainly characterized by Deltaproteobacteria, Enterobacterales, Enterobacteriaceae and Klebsiella spp.; the flora of renal abscess group was mainly characterized by Comamonadaceae, Mycobacteriaceae, Proteus spp., Brevibacillus spp., Cellulosilyticum spp., Lachnospira spp., Leptotrichia spp., Pelomonas spp., Mycobacterium spp., Thermicanus spp. and Saccharimonadaceae spp.. Conclusion 16S rDNA sequencing is superior to traditional culture in the detection of pathogens in liver and renal abscess, there are significant differences in the composition of pathogens between liver and renal abscess, 16S rDNA sequencing is an effective method to deeply understand the characteristics of pathogens in liver and renal abscess.